I'm being told by my ac guy that all that 3 zones mean is that you can shut off certain rooms but my wife insists that it should be able to control temperature in each room indiviadually regardlees of the other rooms. Is 3 tone unit. Any ideas?

A 3 zone system will control all of the vents on 3 lines. In some cases you will have 2-3 or more rooms on a single trunk. In my house, 1 zone is main living level- 6 rooms, 1 is basement-4 rooms, 1 is upstairs-2 rooms. With electric baseboard or some hot water systems, you can have individual t'stats in each room but you would need 1 zone valve per room and thermostat with forced air. 3 zones is usually a good design is the Ac is properly sized.